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A fast numerical method for an advanced electro-chemo-mechanical model is developed which is able to capture phase separation processes in porous materials. This method is applied to simulate lithium-ion battery cells, where the complex microstructure of the electrodes is fully resolved. The intercalation of ions into the popular cathode material LFP leads to a separation into lithium-rich and lithium-poor phases. The large concentration gradients result in high mechanical stresses. A phase-field method applying the Cahn-Hilliard equation is used to describe the diffusion. For the sake of simplicity, the linear elastic case is considered. Numerical tests for fully resolved three-dimensional granular microstructures are discussed in detail.